So I after I pitched my yeast I pushed a rubber bung too far in the carboy. As I tried to get it out it went farther in, long story short it went all the way threw. My question is will this effect the beer at all to have a rubber stopper floating in it during primary fermentation?

I've got a porter sitting in secondary right now that went through primary with a silicone bung and a sample glass in it. Can't say for 100% sure it's not infected, but it was tasty and pellicle-free when I racked it...

Gee, I've never heard of anyone poking the bung into the fermenter before. Did you do that on purpose? What kind of flavor profile are you expecting? I would expect you would get a much more pronounced rubber flavor if you put it in the boil, instead of putting it in primary. Of course, there's also the possibility of creating a "bung tea" and putting that in the secondary. Personally I would use the Italian bungs. Much more of a aromatic flavor.